Answer:
It doesn't - you'll have to buy a powerlet adapter if you want to plug in to the port. Note that if you go this route, there's a key on/off procedure you'll have to follow or the port will shut off and the battery won't receive a charge.
Anyway, I've had six BMWs, two with CANbus electronics whose manuals included the same disclaimer you mentioned. I was wary too, but after some research I found I was able to safely use the Battery Tender with it's included harness kit to charge directly to the battery, which I did. Note that Battery Tender ships two different harness kits; one with an in-line fuse, one without (I think the BT Jr. doesn't have the in-line fuse). I recommend only using the fused model.
BMW sells an OEM branded charger you can plug directly in to the factory powerlet, but many prefer the Battery Tender and think it's a better product. I'm one of them, as are quite a few good staffers I know at BMW dealerships around the country.
If you'd like more info, you'll find a lot of chatter on this topic on sites like ADVrider and other BMW specific forums - just do a Google search.